The genetic markers associated with economic traits have been widely explored for animal breeding. Among these markers, single-nucleotide polymorphism (SNPs) are gradually becoming a prevalent and effective evaluation tool. Since SNPs only focus on the genetic sequences of interest, it thereby reduces the evaluation time and cost. Compared to traditional approaches, SNP genotyping techniques incorporate informative genetic background, improve the breeding prediction accuracy and acquiesce breeding quality on the farm. This article therefore reviews the typical procedures of animal breeding using SNPs and the current status of related techniques. The associated SNP information and genotyping techniques, including microarray and Lab-on-a-Chip based platforms, along with their potential are highlighted. Examples in pig and poultry with different SNP loci linked to high economic trait values are given. The recommendations for utilizing SNP genotyping in nimal breeding are summarized.

Regional specificity allows different skin regions to exhibit different characteristics, enabling complementary functions to make effective use of the integumentary surface. Chickens exhibit a high degree of regional specificity in the skin and can serve as a good model for when and how these regional differences begin to emerge. We used developing feather and scale regions in embryonic chickens as a model to gauge the differences in their molecular pathways. We employed cosine similarity analysis to identify the differentially regulated and co-regulated genes. We applied low cell techniques for expression validation and chromatin immunoprecipitation (ChIP)-based enhancer identification to overcome limited cell availabilities from embryonic chicken skin. We identified a specific set of genes demonstrating a high correlation as being differentially expressed during feather and scale development and maturation. Some members of the WNT, TGF-beta/BMP, and Notch family known to be involved in feathering skin differentiation were found to be differentially regulated. Interestingly, we also found genes along calcium channel pathways that are differentially regulated. From the analysis of differentially regulated pathways, we used calcium signaling pathways as an example for further verification. Some voltage-gated calcium channel subunits, particularly CACNA1D, are expressed spatio-temporally in the skin epithelium. These calcium signaling pathway members may be involved in developmental decisions, morphogenesis, or epithelial maturation. We further characterized enhancers associated with histone modifications, including H3K4me1, H3K27ac, and H3K27me3, near calcium channel-related genes and identified signature intensive hotspots that may be correlated with certain voltage-gated calcium channel genes. We demonstrated the applicability of cosine similarity analysis for identifying novel regulatory pathways that are differentially regulated during development. Our study concerning the effects of signaling pathways and histone signatures on enhancers suggests that voltage-gated calcium signaling may be involved in early skin development. This work lays the foundation for studying the roles of these gene pathways and their genomic regulation during the establishment of skin regional specificity.

Average daily gain (ADG) and feed efficiency (FE) are important factors for assessing productivity in farm animals. Myostatin (MSTN), previously called GDF8, is a member of transforming growth factor β (TGFβ) superfamily. It is a negative regulator for both embryonic development and adult homeostasis of skeletal muscle. In this study, the genotypes of MSTN g.435G > A and g.447A > G SNPs in Duroc pigs were determined. The 435GG/447AA individually had significantly higher ADG (P < 0.01), body weight at 70 d (P < 0.05) and 150 d (P < 0.01), and a lower age at 110 kg (P < 0.01) than 435AA/447GG individuals. Dose dependent genetic additive effects were found for the negative effects of the 435A/447 G allele for ADG and body weight on 70 d and 150 d. The 435A/447 G allele also increased the age at 110 kg about 1.47 and 4.53% for 1 and 2 copies, respectively. The MSTN 435 G/447A allele increased the age at 110 kg about 1.41 and 4.47% for 1 and 2 copies, respectively. Overall, the two mutated MSTN 435A/447G allele had negative effects on ADG (P < 0.01), body weight at 70 d (P < 0.05), and 150 d (P < 0.001) and increased the age at 110 kg (P < 0.001). The present study provided evidence that MSTN g.435G > A and g.447A > G affected growth in Duroc pigs. The effects of the mutated alleles were additive with the maximal effects resulting from two copies of the wild-type allele. Selection for the 435 G/447A allele is expected to increase ADG, body weight and decrease the age at 110 kg in Duroc pigs and might be used in porcine breeding programs.